How To Extract 2-Fold, 3-Fold And 4-Fold Degenerate Amino Acids From A Fasta File?

Question

[anin.gregory]

Is there any easy script to pull 2-fold, 3-fold, and 4-fold degenerate amino acids from a fasta file?

Answer 1

[Asaf]

I don't know if this will suffice you but the program cusp of EMBOSS counts the number of times each codon appears in a nucleotide sequence. You will then get a table with the codon, AA, frequency and counts and from here it's easy to select the AA you want according to 2,3, or 4 fold.